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I respond somewhat with trepidation given that you did not take my advice previously; however, in case anyone else is wondering—I would not do this. In the absence of head motion, the T1w/T2w ratio will exactly cancel the receive field and will attenuate the transmit field (more on this very soon). Algorithmic bias correction generally assumes that tissues are homogeneous in intensity (usually white matter), but the whole point of studying T1w/T2w cortical myelin maps is to look at the inhomogeneity in grey matter. White matter also has real tissue inhomogeneity in T1w and T2w images, and by bias correcting the T1w/T2w map, you would be putting the opposite of the white matter pattern into the grey matter. This confound with bias correction was why I developed the T1w/T2w ratio in the first place.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Marina Fernández marina.fdez.alvarez@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 22, 2021 at 6:50 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] bias field correction and intensity normalization

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Dear experts,

I would like to create myelin maps calculating the T1w/T2w ratio. Should

I apply bias field correction and intensity normalization (i.e., "nu

correction" in the Freesurfer pipeline) to T1w and T2w images separately

before calculating the T1w/T2 ratio?

I applied nu correction to T1w images and worked fine but results were

weird when nu correction was applied applied to T2w images. I am not

sure if nu correction must only be applied to T1w images for this

purpose, or if I have to modify some parameters to apply nu correction

to T2w images.

Thank you in advance for your help.

Best,

Marina

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